Conjunctiva-associated lymphoid tissue (CALT) is a part of the eye-associated lymphoid tissue (EALT) at the ocular surface. Its lymphoid follicles are usually characterized by using light microscopy, but its ultrastructure remains largely unknown. In this study, flat whole-mount conjunctival tissues ( n = 42) from 21 young adult rabbits were investigated native in reflected light, and further stained and cleared ( n = 6), in paraffin histology sections ( n = 6), scanning electron microscopy (SEM, n = 4) and transmission electron microscopy (TEM, n = 4). Secondary lymphoid follicles accumulated into a dense group nasally towards the lacrimal punctum of the lower lid. High endothelial venules